Python学习教程（四）

1年前发布

Python 教程

陈同 (chentong_biology@163.com)

欢迎来到Python的世界，本教程将带你遨游Python，领悟Python的魅力。本教程专注于帮助初学者，尤其是生物信息分析人员快速学会Python的常用功能和使用方式，因此只精选了部分Python的功能，请额外参考Python经典教程A byte of python和它的中文版来更好的理解Python. 本文档的概念和文字描述参考了A byte of python(中文版)，特此感谢。

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 2.0 Generic License.

实战练习（一）

背景知识

1. FASTA文件格式

>seq_name_1

sequence1

>seq_name_2

sequence2

2. FASTQ文件格式

@HWI-ST1223:80:D1FMTACXX:2:1101:1243:2213 1:N:0:AGTCAA

TCTGTGTAGCCNTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCATGCA

+

BCCFFFFFFHH#4AFHIJJJJJJJJJJJJJJJJJIJIJJJJJGHIJJJJJJJJJ

作业 (一)

给定FASTA格式的文件(test1.fa 和 test2.fa)，写一个程序 cat.py 读入文件，并输出到屏幕
- open(file)
- for .. in loop
- print
- the amazng , or strip() function
- 用到的知识点
给定FASTQ格式的文件(test1.fq), 写一个程序 cat.py 读入文件，并输出到屏幕
- 同上
- 用到的知识点
写程序 splitName.py, 读入test2.fa, 并取原始序列名字第一个空格前的名字为处理后的序列名字，输出到屏幕
- split
- 字符串的索引

用到的知识点

输出格式为：

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctg.......

写程序 formatFasta.py, 读入test2.fa，把每条FASTA序列连成一行然后输出
- join
- strip

用到的知识点

输出格式为:

>NM_001011874 gcggcggcgggc......TCCGCTG......GCGTTCACC......CGGGGTCCGGAG

写程序 formatFasta-2.py, 读入test2.fa，把每条FASTA序列分割成80个字母一行的序列
- 字符串切片操作
- range

用到的知识点

输出格式为

>NM_001011874 gcggcggcgc.(60个字母).TCCGCTGACG #(每行80个字母) acgtgctacg.(60个字母).GCGTTCACCC ACGTACGATG(最后一行可不足80个字母)

写程序 sortFasta.py, 读入test2.fa, 并取原始序列名字第一个空格前的名字为处理后的序列名字，排序后输出
- sort
- dict
- aDict[key] = []
- aDict[key].append(value)
- 用到的知识点
提取给定名字的序列
- 用到的知识点
- print >>fh, or fh.write()
- 取模运算，4 % 2 == 0
- 写程序 grepFasta.py, 提取fasta.name中名字对应的test2.fa的序列，并输出到屏幕。
- 写程序 grepFastq.py, 提取fastq.name中名字对应的test1.fq的序列，并输出到文件。
写程序 screenResult.py, 筛选test.expr中foldChange大于2的基因并且padj小于0.05的基因
- 逻辑与操作符 and
- 文件中读取的内容都为字符串，需要用int转换为整数，float转换为浮点数
- 用到的知识点
写程序 transferMultipleColumToMatrix.py 将文件(multipleColExpr.txt)中基因在多个组织中的表达数据转换为矩阵形式
- aDict[‘key’] = {}
- aDict[‘key’][‘key2’] = value
- if key not in aDict
- aDict = {‘ENSG00000000003’: {“A-431”: 21.3, “A-549”, 32.5,…},”ENSG00000000003”:{},}

用到的知识点

输入格式(只需要前3列就可以)

Gene    Sample  Value   Unit    Abundance ENSG00000000003 A-431   21.3    FPKM    Medium ENSG00000000003 A-549   32.5    FPKM    Medium ENSG00000000003 AN3-CA  38.2    FPKM    Medium ENSG00000000003 BEWO    31.4    FPKM    Medium ENSG00000000003 CACO-2  63.9    FPKM    High ENSG00000000005 A-431   0.0     FPKM    Not detected ENSG00000000005 A-549   0.0     FPKM    Not detected ENSG00000000005 AN3-CA  0.0     FPKM    Not detected ENSG00000000005 BEWO    0.0     FPKM    Not detected ENSG00000000005 CACO-2  0.0     FPKM    Not detected

输出格式

Name    A-431    A-549    AN3-CA    BEWO    CACO-2 ENSG00000000460    25.2    14.2    10.6    24.4    14.2 ENSG00000000938    0.0    0.0    0.0    0.0    0.0 ENSG00000001084    19.1    155.1    24.4    12.6    23.5 ENSG00000000457    2.8    3.4    3.8    5.8    2.9

写程序 reverseComplementary.py计算序列 ACGTACGTACGTCACGTCAGCTAGAC的反向互补序列
- reverse
- list(seq)
- 用到的知识点
写程序 collapsemiRNAreads.py转换smRNA-Seq的测序数据
- 输入文件格式(mir.collapse, tab-分割的两列文件，第一列为序列，第二列为序列被测到的次数)
```
  ID_REF        VALUE   ACTGCCCTAAGTGCTCCTTCTGGC        2   ATAAGGTGCATCTAGTGCAGATA        25   TGAGGTAGTAGTTTGTGCTGTTT        100   TCCTACGAGTTGCATGGATTC        4
```
- 输出文件格式 (mir.collapse.fa, 名字的前3个字母为样品的特异标示，中间的数字表示第几条序列，是序列名字的唯一标示，第三部分是x加每个reads被测到的次数。三部分用下划线连起来作为fasta序列的名字。)
```
  >ESB_1_x2   ACTGCCCTAAGTGCTCCTTCTGGC   >ESB_2_x25   ATAAGGTGCATCTAGTGCAGATA   >ESB_3_x100   TGAGGTAGTAGTTTGTGCTGTTT   >ESB_4_x4   TCCTACGAGTTGCATGGATTC
```
简化的短序列匹配程序 (map.py) 把short.fa中的序列比对到ref.fa, 输出短序列匹配到ref.fa文件中哪些序列的哪些位置
- find
- 用到的知识点
- 输出格式 (输出格式为bed格式，第一列为匹配到的染色体，第二列和第三列为匹配到染色体序列的起始终止位置（位置标记以0为起始，代表第一个位置；终止位置不包含在内，第一个例子中所示序列的位置是(199,208](前闭后开，实际是chr1染色体第199-206的序列，0起始). 第4列为短序列自身的序列.)。
- 附加要求：可以只匹配到给定的模板链，也可以考虑匹配到模板链的互补链。这时第5列可以为短序列的名字，第六列为链的信息，匹配到模板链为’+’，匹配到互补链为’-‘。注意匹配到互补链时起始位置也是从模板链的5’端算起的。
```
chr1    199    208    TGGCGTTCA chr1    207    216    ACCCCGCTG chr2    63    70    AAATTGC chr3    0    7    AATAAAT
```
备注：
- 每个提到提到的“用到的知识点”为相对于前面的题目新增的知识点，请综合考虑。此外，对于不同的思路并不是所有提到的知识点都会用着，而且也可能会用到未提到的知识点。但是所有知识点都在前面的讲义部分有介绍。
- 每个程序对于你身边会写的人来说都很简单，因此你一定要克制住，独立去把答案做出，多看错误提示，多比对程序输出结果和预期结果的差异。
- 学习锻炼“读程序”，即对着文件模拟整个的读入、处理过程来发现可能的逻辑问题。
- 程序运行没有错误不代表你写的程序完成了你的需求，你要去查验输出结果是不是你想要的。
关于程序调试
- 在初写程序时，可能会出现各种各样的错误，常见的有缩进不一致，变量名字拼写错误，丢失冒号，文件名未加引号等，这时要根据错误提示查看错误类型是什么，出错的是哪一行来定位错误。当然，有的时候报错的行自身不一定有错，可能是其前面或后面的行出现了错误。
- 当结果不符合预期时，要学会使用print来查看每步的操作是否正确，比如我读入了字典，我就打印下字典，看看读入的是不是我想要的，是否含有不该存在的字符；或者在每个判断句、函数调入的情况下打印个字符，来跟踪程序的运行轨迹。

%%writefile script/cat.py
#作业1和2, cat.py
#包含了三中处理换行符的写法
for line in open("data/test1.fa"):
    print line.strip()

for line in open("data/test2.fa"):
    print line,

for line in open("data/test1.fq"):
    line = line.strip()
    print line

Overwriting script/cat.py

%run script/cat

>NM_001011874 gene=Xkr4 CDS=151-2091 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg >NM_001195662 gene=Rp1 CDS=55-909 AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA >NM_011283 gene=Rp1 CDS=128-6412 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC >NM_0112835 gene=Rp15 CDS=128-6412 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC >NM_001011874 gene=Xkr4 CDS=151-2091 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg aggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTG CCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACC CCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_001195662 gene=Rp1 CDS=55-909 AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGC AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA AGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGT GGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGC TGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACA CAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG >NM_011283 gene=Rp1 CDS=128-6412 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA >NM_0112835 gene=Rp1 CDS=128-6412 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA @HWI-ST1223:80:D1FMTACXX:2:1101:1243:2213 1:N:0:AGTCAA TCTGTGTAGCCNTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCATGCACCACCACNNNCGGCTCATTTGTCTTTNNTTTTTGTTTTGTTCTGTA + BCCFFFFFFHH#4AFHIJJJJJJJJJJJJJJJJJIJIJJJJJGHIJJJJJJJJJJJJJIIJ###--5ABECFFDDEEEEE##,5=@B8?CDD<AD>C:@> @HWI-ST1223:80:D1FMTACXX:2:1101:1375:2060 1:N:0:AGTCAA NTGCTGAGCCACGACAAGGATCCCAGAGGGCCNAGCCCTGCATCTTGTATGGACCAGTTACNCATCAAAAGAGACTACTGTAGGCACCATCAATCAGATC + #1:DDDD;?CFFHDFEEIGIIIIIIG;DHFGG#)0?BFBDHBFF<FCFEFD;@DD@A=7?E#,,,;=(>3;=;;C>ACCC@CCCCCBBBCCAACCCCCCC @HWI-ST1223:80:D1FMTACXX:2:1101:1383:2091 1:N:0:AGTCAA NGTTCGTGTGGAACCTGGCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCTGCGATCTATTGAA + #1=DDFDFHHHHHJGJJJJJJJJJJJJJJJIJIGDHIHIGIJJJJJJJIIIGHHFDD3>BDDBDDDDDDDDDDBDCCBDDDDDDDDDDDBBDDDDEEACD @HWI-ST1223:80:D1FMTACXX:2:1101:1452:2138 1:N:0:AGTCAA NTCTAGGAGGTCTAGAAAGCCCAGGCCACCGGTACAAACATCAAGGGTGTTACGGATGTGCCGCTCTGAACCTCCAGGACGACTTTGATTTCAACTACAA + #4=DFFEFHHHHHJJJJJIJJJJHIIJGJJJJ@GIIJJJJJJIJJJJFGHIIIJJHHHDFFFFDDDDDDDDDDDDCDDDDDDDDDDDCCCEDEDDDDDDD

%%writefile script/splitName.py
#作业3
filename = "data/test2.fa"
for line in open(filename):
    if line[0] == '>':
        lineL = line.split(' ')
        print lineL[0]
    else:
        print line,

Overwriting script/splitName.py

%run script/splitName

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg aggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTG CCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACC CCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_001195662 AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGC AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA AGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGT GGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGC TGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACA CAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG >NM_011283 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA >NM_0112835 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

%%writefile script/formatFasta.py
#作业4
filename = "data/test2.fa"
aList = []
for line in open(filename):
    if line[0] == '>':
        lineL = line.split(' ')
        if aList:
            print ''.join(aList)
            aList = []
        name = lineL[0]
        print name
    else:
        aList.append(line.strip())
#不要忘了最后一个序列
print ''.join(aList)

Overwriting script/formatFasta.py

%run script/formatFasta

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_001195662 AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG >NM_011283 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA >NM_0112835 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

%%writefile script/formatFasta-2.py
#作业5 
filename = "data/test2.fa"
length = 80
aList = []
for line in open(filename):
    if line[0] == '>':
        lineL = line.split(' ')
        if aList:
            seq = ''.join(aList)
            len_seq = len(seq)
            for i in range(0,len_seq,length):
                print seq[i:i+length]
            aList = []
        name = lineL[0]
        print name
    else:
        aList.append(line.strip())
#不要忘了最后一个序列
seq = ''.join(aList)
len_seq = len(seq)
for i in range(0,len_seq,length):
    print seq[i:i+length]

Overwriting script/formatFasta-2.py

%run script/formatFasta-2

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggag gtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTA AGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCT GTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_001195662 AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACC CAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATT CAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTG GTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGT AAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCT CCCACAATAAGAAGGTGCTG >NM_011283 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATT TACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATG ATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTC TGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATC ACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA >NM_0112835 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATT TACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATG ATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTC TGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATC ACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

%%writefile script/sortFasta.py
#作业6
aDict = {}

filename = "data/test2.fa"

for line in open(filename):
    if line[0] == '>':
        key = line.split()[0]
        aDict[key] = []
    else:
        aDict[key].append(line.strip())
#--------END reading--------------------
keyL = aDict.keys()
keyL.sort()

for key in keyL:
    print "%s\n%s" % (key, ''.join(aDict[key]))

Overwriting sortFasta.py

%run script/sortFasta

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_001195662 AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG >NM_011283 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA >NM_0112835 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

%%writefile script/grepFasta.py
#作业7.1
aDict = {}

seqFile = "data/test2.fa"
nameFile = "data/fasta.name"

for line in open(seqFile):
    if line[0] == '>':
        key = line.split()[0][1:] #注意去掉开头的'>'，只取序列的名字
        aDict[key] = []  #字典的值是一个列表
    else:
        aDict[key].append(line.strip())
#--------END reading--------------------
for line in open(nameFile):
    name = line.strip()
    print ">%s\n%s" % (name, ''.join(aDict[name]))

Overwriting grepFasta.py

%run script/grepFasta.py

>NM_001011874 gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG >NM_011283 AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

%%writefile script/grepFastq.py
#作业7.2
seqFile = "data/test1.fq"
nameFile = "data/fastq.name"

aDict = {}
count = 0
for line in open(seqFile):
    count += 1
    if count % 4 == 1:
        name = line.strip()[1:] #去掉开头的@
        aDict[name] = [line] #存储名字行
    else:
        aDict[name].append(line)
#-------END reading----------这行知识注释，可有可无------
for line in open(nameFile):
    name = line.strip()
    print ''.join(aDict[name]),

Overwriting grepFastq.py

%run script/grepFastq

@HWI-ST1223:80:D1FMTACXX:2:1101:1243:2213 1:N:0:AGTCAA TCTGTGTAGCCNTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCATGCACCACCACNNNCGGCTCATTTGTCTTTNNTTTTTGTTTTGTTCTGTA + BCCFFFFFFHH#4AFHIJJJJJJJJJJJJJJJJJIJIJJJJJGHIJJJJJJJJJJJJJIIJ###--5ABECFFDDEEEEE##,5=@B8?CDD<AD>C:@> @HWI-ST1223:80:D1FMTACXX:2:1101:1375:2060 1:N:0:AGTCAA NTGCTGAGCCACGACAAGGATCCCAGAGGGCCNAGCCCTGCATCTTGTATGGACCAGTTACNCATCAAAAGAGACTACTGTAGGCACCATCAATCAGATC + #1:DDDD;?CFFHDFEEIGIIIIIIG;DHFGG#)0?BFBDHBFF<FCFEFD;@DD@A=7?E#,,,;=(>3;=;;C>ACCC@CCCCCBBBCCAACCCCCCC @HWI-ST1223:80:D1FMTACXX:2:1101:1383:2091 1:N:0:AGTCAA NGTTCGTGTGGAACCTGGCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCTGCGATCTATTGAA + #1=DDFDFHHHHHJGJJJJJJJJJJJJJJJIJIGDHIHIGIJJJJJJJIIIGHHFDD3>BDDBDDDDDDDDDDBDCCBDDDDDDDDDDDBBDDDDEEACD @HWI-ST1223:80:D1FMTACXX:2:1101:1452:2138 1:N:0:AGTCAA NTCTAGGAGGTCTAGAAAGCCCAGGCCACCGGTACAAACATCAAGGGTGTTACGGATGTGCCGCTCTGAACCTCCAGGACGACTTTGATTTCAACTACAA + #4=DFFEFHHHHHJJJJJIJJJJHIIJGJJJJ@GIIJJJJJJIJJJJFGHIIIJJHHHDFFFFDDDDDDDDDDDDCDDDDDDDDDDDCCCEDEDDDDDDD

%%writefile script/screenResult.py
#作业8
file = "data/test.expr"

head = 1 #This is used to indicate there is one head line needing to skip
for line in open(file):
    if head:
        head -= 1
        continue
    #-----Begin data lines------
    lineL = line.split()

    foldChange = float(lineL[9])
    adjP = float(lineL[12])
    if foldChange > 2 and adjP < 0.05:
        print lineL[0]

Overwriting screenResult.py

%run script/screenResult

Novel00011 Novel00043 Novel00047 Novel00077 Novel00079 Novel00080 Novel00084 Novel00085 Novel00086 Novel00087 Novel00090 Novel00124 Novel00148 Novel00156 Novel00162 Novel00166

%%writefile script/transferMultipleColumToMatrix.py
#作业9
file = "data/multipleColExpr.txt"
head = 1
tissueSet = set()
aDict = {}
for line in open(file):
    if head: #skip header line
        head -= 1
        continue
    #-------------------------------
    lineL = line.split()
    gene = lineL[0]
    tissue = lineL[1]
    expr = lineL[2]
    if gene not in aDict:
        aDict[gene] = {}
    assert tissue not in aDict[gene], "Duplicate tissues"
    aDict[gene][tissue] = expr
    tissueSet.add(tissue)
#---END reading----------------------------
tissueL = list(tissueSet)
tissueL.sort()
print "Gene\t%s" % '\t'.join(tissueL)

for gene, tissueD in aDict.items():
    exprL = [gene]
    for tissue in tissueL:
        exprL.append(tissueD[tissue])
    print '\t'.join(exprL)

Overwriting transferMultipleColumToMatrix.py

%run script/transferMultipleColumToMatrix

Gene    A-431    A-549    AN3-CA    BEWO    CACO-2 ENSG00000000460    25.2    14.2    10.6    24.4    14.2 ENSG00000000938    0.0    0.0    0.0    0.0    0.0 ENSG00000000457    2.8    3.4    3.8    5.8    2.9 ENSG00000000419    73.8    38.6    33.9    53.7    155.5 ENSG00000000003    21.3    32.5    38.2    31.4    63.9 ENSG00000000005    0.0    0.0    0.0    0.0    0.0

%%writefile script/reverseComplementary.py
#作业10
str1 = "ACGTACGTACGTCACGTCAGCTAGAC"

ATCG_dict = {'A':'T','T':'A','C':'G','G':'C', 'a':'t','t':'a','c':'g','g':'c'}

tmpL = []
for i in str1:
    tmpL.append(ATCG_dict[i])
tmpL.reverse()
print ''.join(tmpL)

Overwriting reverseComplementary.py

%run script/reverseComplementary

GTCTAGCTGACGTGACGTACGTACGT

%%writefile script/collapsemiRNAreads.py
#作业11
smRNA_file = "data/mir.collapse"

head = 1
sample = 'ESB'
lineno = 0
for line in open(smRNA_file):
    if head:
        head -= 1
        continue
    #----end skip header line---
    seq, value = line.split()
    lineno += 1
    print ">%s_%d_x%s\n%s" % (sample, lineno, value, seq)

Overwriting collapsemiRNAreads.py

%run script/collapsemiRNAreads

>ESB_1_x2 ACTGCCCTAAGTGCTCCTTCTGGC >ESB_2_x2 ATAAGGTGCATCTAGTGCAGATA >ESB_3_x1 TGAGGTAGTAGTTTGTGCTGTTT >ESB_4_x1 TCCTACGAGTTGCATGGATTC >ESB_5_x1 ACCGGGTGGAGCCGCCGCA >ESB_6_x1 ACTGCCCTAAGTGCTCCTTCTGGT >ESB_7_x1 TACAGGGCTGGGGATGG >ESB_8_x1 CCCTGGATGCTGTAGGATG >ESB_9_x1 AAAATGCTACTACTTTTGAGTC >ESB_10_x1 TCCCTGGTGGTCTAGTGGCTAGGAT >ESB_11_x4 CTCTTAGATCGATGTGGTGCTC >ESB_12_x1 TTGGTGGTTCAGTGGTA >ESB_13_x1 TCACAATTCCCCTATACCATGGGCCAT >ESB_14_x1 CAAATGCTAGGGTTGGTGG >ESB_15_x4 AGGCAGCTTCCACAGCA >ESB_16_x3 GCACTGAGATGGAGTGGTGTAA >ESB_17_x3 CTCCATTTGTTTGATGATGGA >ESB_18_x1 GCACTGAGATGGAGTGGTGTAT >ESB_19_x2 AGTGCCCAGAGTTTGTAGTGT >ESB_20_x1 ATAAGGTGCATCTAGTGCTGTTAGA >ESB_21_x9 AAAATGCTTCCACTTTGTGTG >ESB_22_x2 GGTAATTCTAGAGCTAATACATGCCG >ESB_23_x6 CCGGGCGGAAACACCA >ESB_24_x1 TGAAAGGCTGACCCGCCGGGC >ESB_25_x1 TTCGTACAGTGGTCGTAAGTTCGTGC >ESB_26_x1 GGTTAGCACTCTGGACTC

%%writefile script/map.py
#作业12
ref = "data/ref.fa"
short = "data/short.fa"

refD = {}
for line in open(ref):
    if line[0] == '>':
        name = line[1:-1]
        assert name not in refD
        refD[name] = []
    else:
        refD[name].append(line.strip())
#---------END reading----------------
for key, valueL in refD.items():
    refD[key] = ''.join(valueL)
#------------------------------------
for line in open(short):
    if line[0] == '>':
        pass
    else:
        seq = line.strip()
        len_seq = len(seq)
        for key, value in refD.items():
            pos = value.find(seq)
            while pos != -1:
                print "%s\t%d\t%d\t%s" % (key, pos, pos+len_seq, seq)
                current = pos + 1
                newpos = value[current:].find(seq)
                if newpos == -1:
                    break
                pos = current + newpos

Overwriting map.py

%run script/map

chr1    199    208    TGGCGTTCA chr1    207    216    ACCCCGCTG chr2    63    70    AAATTGC chr3    0    7    AATAAAT chr3    66    74    CCACACAA chr3    206    214    ATATCACT chr2    163    171    ATATCACT chr3    417    423    AGAGGA chr2    374    380    AGAGGA chrX    137    143    AGAGGA

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